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Preview of the current [NeoNet C14 dates dataset](#panel.data), in red, covering the Late Mesolithic/Early Neolithic transition of the North Central-Western Mediterranean watershed

Preview of the current NeoNet C14 dates dataset, in red, covering the Late Mesolithic/Early Neolithic transition of the North Central-Western Mediterranean watershed

1 Presentation

The NeoNet app aims to contribute to the study the pioneering front of the farming live-style (i.e., Neolithic) by focusing our study on the mobile border between the Last Hunter-Gathers economy and the Early Neolithic (ca. 7,000 BC to 3,500 BC) in the Central and Western Mediterranean. The interactive web app facilitates the selection of absolute dates (c14 dates) by providing selection tools for:

This static website is a tutorial for the RShiny NeoNet app. Both have been generated with R, from a perspective of FAIR Science and collaborative working. The app has been developed in the frame of the NeoNet work group. We will see how it works, what is the format dataset and what are our objectives

2 NeoNet app

The app is a RShiny hosted on the Università di Pisa server. The app is divided into five (5) panels:

  1. map panel: spatial filtering with selection menus on dates
  2. calib panel: calibration of the selected dates
  3. data panel: the whole dataset
  4. biblio panel: bibliographical references
  5. infos panel: credits and link to the webpage handbook of the app

2.1 1. map panel

The panel map is a geographical window provided by the Leaflet package. This panel is used for selection of radiocarbon dates by location, by chronology, by quality of dates. Once selected, dates can be calibrated

The different menus of the map panel

The different menus of the map panel

The current functions are:

  • Fig. @ref(fig:panel-map1), red box, top-left button group C14 on map: allows to cluster dates by spatial proximities (Marker Clusters)

  • Fig. @ref(fig:panel-map1), pink box, top-right layer button: allows to change the basemap. By default, the basemap is OSM, an OpenStreetMap general basemap, but it can be switch to Topo, an ESRI topographical basemap

  • Fig. @ref(fig:panel-map1), grey box, bottom inline text: reactive count of selected dates and select sites

  • Fig. @ref(fig:panel-map1), green box, bottom table: reactive datatable (DT package) listing all the dates within the map extent (ROI) and the optional selection menus (tpq/taq, material life duration, maximum SD, periods, selection shapes)

2.1.1 select by location

By default only the data within the window extent (ROI) will be selected. But selection shapes can be drawn inside this ROI to have a spatial intersection:

Fig. @ref(fig:panel-map1), black box, top-left draw toolbar: selection shapes, polygons and rectanges, can freeze the date selection inside a given ROI. They can be removed with the trash button. All the dates inside the ROI and selected with the others filters will be visible on the map, but only those inside the selections shapes will be calibrated

selection inside a shape, here a single polygon. Before shape selection: 190 sites and 895 dates. After shape selection: 13 sites and 68 dates

2.1.1.1 retrieve coordinates from the map

As said, the default basemap of the app is OSM. It offers a well documented basemap where archaeological sites are sometimes already located, like the Ligurian site of Grotta della Pollera. Clicking on the map show the lat/long coordinates of the current point (under the tpq/tap slider). These coordinates can then be copied and used to modify the NeoNet dataset

get coordinates by clicking on the map

2.1.2 select by chronology

  • Fig. @ref(fig:panel-map1), brown box, top-right checkboxes: allow to select dating by periods. The orange box, bottom-left legend, is reactive and update depending on selected periods

  • Fig. @ref(fig:panel-map1), blue box, bottom-left slider: allows to subset a range of accepted dates between a tpq and a taq (in cal BC)

2.1.3 select by dates quality

  • Fig. @ref(fig:panel-map1), purple box, bottom-right checkboxes and slider: a group of menus for selection on the material life duration and max accepted SD:
    • relatively to the duration of their material (short to long-life material)
    • below a maximum accepted threshold for the standard deviations (SD) for the dates

2.1.4 calibrate one or various dates

The dates displayed in the table of the map panel will be calibrate when one of them has been clicked.

click on a date to calibrate a selected group of dates

2.2 2. calib panel

The panel calib is used for analysis. Calibration of selected dates are done on-the-fly with the R package rcarbon. If the dates are numerous (e.g., > 100) the computing time could take times, be patient.

calibrate dates

This date which have been clicked on the map panel will be shown bolded on the output figure

2.2.1 c14 group by filter

The only selection which can be done is on the top-center radio button (Fig. @ref(fig:panel-calib), red box). The c14 group by filter allows to plot dates and to sum their probability densities depending on different levels of grouping:

  • LabCode: each radiocarbon date is plot separately (by default)

  • SiteName and PhaseCode: dates from the same site, having the same archaeological unit (layer, structure, etc.), are summed. See the PhaseCode field.

  • SiteName and Period: dates from the same site, having the same period are summed

  • Period: dates having the same period are summed

  • All C14: all dates are summed

The different menus of the calib panel

The different menus of the calib panel

2.2.2 plot area output

The plot area (Fig. @ref(fig:panel-calib), orange box) shows dynamically the SPD of the cabibrated dates seriated on their weighted means. The top-right button Download (Fig. @ref(fig:panel-calib), green box) allows to export the last plot in a PNG image

2.3 3. data panel

The complete dataset from the GitHub c14data.tsv file (a dataframe with tab-separated values). Today, the dataset counts 2478 dates:

Dates sample
SiteName Country Period PhaseCode LabCode C14Age C14SD Material MaterialSpecies tpq taq Longitude Latitude bib bib_url
208 Arma dell’Aquila Italy EN RS2 OxA-2365-51 5738 33 bone (human) Homo sapiens -4407 -4775 8.32967 44.20471 Sparacello et al. 2019 https://doi.org/10.1016/j.quaint.2019.02.003
2366 Vassieux en Vercors France EN SONDAGE S5 EB A -50 CM Ly-799 5990 60 wood charcoal Wood charcoal (unidentified) (lot) -4607 -5210 5.37000 44.89000 Shennan & Steele 2000 Shennan00
626 Favella della Corte Italy EN Ditch Z, Structure A Beta-71633 6940 40 cereal Cerealia sp. (unidentified) -5663 -5988 16.43746 39.68409 Mazzucco et al. 2020 https://doi.org/10.1371/journal.pone.0232455.s002
115 Grotta Continenza Italy EN Con 20 R-2938 6570 63 wood charcoal Wood charcoal (unidentified) -5309 -5718 13.56307 41.96167 Serradimigni et al. 2016 https://doi.org/10.1016/j.quaint.2016.12.027

At first, these data were recorded in an Excel spreadsheet (c14 spreadsheet) in order to facilitate their editing (filter, sorting, fill). Then a R function reads this spreadsheet, calculates the tpq and taq (in cal BC) of each uncal BP (with Bchron), and converts it into a .tsv file. As data came from various publications, a homogenization the different values (material, cultures, bibliographical references, etc.) has been done. The dataset mandatory fields are:

  • SiteName: the site name
  • coordinates (two fields)
  • Longitude: in decimal degrees (ex: 1.0451)
  • Latitude: in decimal degrees (ex: 43.9213)
  • Period: a value as following: LM (Late Mesolithic), UM (Undefined Mesolithic), LMEN (Late Mesolithic/Early Neolithic), EN (Early Neolithic), MN (Middle Neolithic), LN (Late Neolithic), UN (Undefined Neolithic)
  • PhaseCode: a code for the dating stratigaphical unit and/or structure
  • C14Age: a numerical radiocarbon dating in BP
  • C14SD: the standard deviation (SD) of the radiocarbon dating
  • LabCode: the unique identifier of the radiocarbon dating
  • Material: a value from the material.life spreadsheet
  • MaterialSpecies: a specification of the field Material
  • tpq: the terminus post quem of the radiocarbon dating in cal BC
  • taq: the terminus ante quem of the radiocarbon dating in cal BC
  • bibliographical references (two fields)

The recommended fields are:

  • Culture: a specification of the field Period

The others fields (if there’s any) only concern the EUROEVOL_R app

2.3.0.1 mandatory fields

Here we explain more precisely some of the mandatory fields

2.3.0.1.1 Longitude and Latitude

In in decimal degrees and a precision of four (4) decimal digits (ex: 1.0453, 43.9211). Since the modeling is supra-regional, the app does not need to record dates with high accuracy geographical coordinates. At the minimum, this accuracy can be a location inside the departmental/county boundaries (how to retrieve better coordinates from the map)

2.3.0.1.2 PhaseCode

The PhaseCode field provide a more precise archaeological context than the site name. It is useful for layer/structure C14 grouping. Most of the time, it correspond to an archaeological layer or structure

PhaseCode
C5
C7-8
foyer 7
niv. II
…

Values of this field need to be homogeneized (for example: C.5 or layer 5 -> C5) – at first for the same sites, in order to group them – then for the whole dataset. The n/a value (i.e., not available) is reserved to dates without intra-site contextual information

2.3.0.1.3 LabCode

LabCode (i.e., laboratory code) should be unique. Their conventional syntax is ‘AbrevLab-number’, respecting the case letters (upper case and lower case). For example:

LabCode
Beta-103487
CSIC-1133
ETH-15984
Gif-1855
GrN-6706
KIA-21356
LTL-13440A
Ly-11338
MC-2145
OxA-9217
Poz-18393
…

See also the list of laboratories. Exceptionally, if a date has no LabCode – e.g., the ‘Sep-H3 mix’ from Fontbregoua, 6082 +/- 35 BP – the convention is to use the PhaseCode (e.g., ‘Sep-H3 mix’) with an underscore as a prefix (e.g., ’_Sep-H3 mix’) to get an unique key.

2.3.0.1.4 bib and bib_url

Every radiocarbon date should be referenced with a short plain text bibliographical reference (bib field) and a DOI, or a BibTex key (bib_url field). We favor the earliest mention of the radiocarbon date.

2.3.0.1.4.1 bib

The plain text that will be plot for each radiocarbon date under the bibliographical reference section. Basically the name of the author(s) and the publication year, for example Guilaine et al. 1993, Binder 2018 or Manen et Sabatier 2013. The values of this field can be the same for two different publications (e.g. Delibrias et al. 1982 refers to two different publications the same year)

2.3.0.1.4.2 bib_url

Either a DOI (starting with “10”) or a unique BibTeX key. We favor the DOI as a unique bibliographical reference. The values of this field should be unique for a single publication (e.g. the BibTeX keys Delibrias82 and Delibrias82a). For example:

tpq taq select RedNeo bib bib_url
-6086 -5923 VRAI 1 Binder et al. 2018 https://doi.org/10.4312/dp.44.4
… … … … … …

When the DOI is lacking, the bibliographical reference should be include into the BibTex document references.bib with the name of the first author and the two last digits of the year:

@book{Guilaine93,
  title={Dourgne: derniers chasseurs-collecteurs et premiers {\'e}leveurs de la Haute-Vall{\'e}e de l'Aude},
    author={Guilaine, Jean and Barbaza, Michel},
    year={1993},
    publisher={Centre d'anthropologie des soci{\'e}t{\'e}s rurales; Arch{\'e}ologie en Terre d'Aude}
  }

The key of this reference is added to the bib_url field. For example, the key value Guilaine93 from the c14 spreadsheet will match this complete reference

tpq taq select RedNeo bib bib_url
-3330 -2492 FAUX 1 Guilaine et al. 1993 Guilaine93
… … … … … …

2.3.1 correspondance tables

The NeoNet app makes joins to two tables in order to retrieve information and to provide a handy user interface

2.3.1.1 material.life

Material life duration are read from the GitHub c14_material_life.tsv file. The two fields show the material type (column 1) and the material life duration (column 2), for example:

material.type life.duration
Drusch - trilladura long.life
Agla long.life
Angiosperma long.life
animal bone short.life
animal hair short.life
antler short.life

This thesaurus is used both by the NeoNet app and the EUROEVOL_R app. Specifically, the NeoNet uses these values:

material.type description
CE Cerealia
F Fauna
H Human
OR Organic
SE Seed
SH Shell
WC Wood charchoal

In the NeoNet app, this dataset is rendered with the (DT package) allowing sorting and filtering tools

2.4 4. biblio panel

Bibliographical references from the GitHub c14refs.tsv file. If only exist a BibTeX key, and no DOI, this file results of the join between the bib_url field of the C14 spreadsheet and the references.bib. If the DOI exists, the full bibliographical reference is file:

Bibliographical references sample
short.ref key.or.doi long.ref
Navarrete et al., 2017 10.1002/oa.2598 Navarrete, V., Colonese, A. C., Tornero, C., Antolín, F., Von Tersch, M., Eulàlia Subirà, M., … Saña, M. (2017). Feeding Management Strategies among the Early Neolithic Pigs in the NE of the Iberian Peninsula. International Journal of Osteoarchaeology, 27(5), 839–852. doi:10.1002/oa.2598
Terna et al. 2016 10.1016/j.epsl.2016.05.003 Tema, E., Ferrara, E., Camps, P., Conati Barbaro, C., Spatafora, S., Carvallo, C., & Poidras, T. (2016). The Earth’s magnetic field in Italy during the Neolithic period: New data from the Early Neolithic site of Portonovo (Marche, Italy). Earth and Planetary Science Letters, 448, 49–61. doi:10.1016/j.epsl.2016.05.003
Bonizzoni et al. 2009 10.1111/j.1475-4754.2008.00412.x BONIZZONI, L., BRUNI, S., GIROD, A., & GUGLIELMI, V. (2009). ARCHAEOMETRIC STUDY OF SHELLS OF HELICIDAE FROM THE EDERA CAVE (NORTHEASTERN ITALY). Archaeometry, 51(1), 151–173. doi:10.1111/j.1475-4754.2008.00412.x
Guerrero 1996 Guerrero96

In the NeoNet app, these BibTex references are rendered in HTML with an APA citation format (field long.ref) with the read.bib() and the markdown() functions (among others)

2.5 5. infos panel

Infos, credits and link to this webpage (https://zoometh.github.io/C14/neonet)

3 Collaborative work

NeoNet workgroup, and NeoNet app, aim to facilitate contributions in a perspective of FAIR Science. In practical terms, we have planned to:

3.1 Contributions

Currently, the NeoNet database and app received the contributions of the NeoNet workgroup collaborators:

3.1.1 How to contribute to the app

The development version of the app is on GitHub: zoometh/neonet. You can check the contribution rules and the relevant license

The next planned development concerns the construction of a chronological model with Bayesian statistics for the different PhaseCode within a single site. Specifically, this means to integrate RChronoModel functions during the calibration process (calib panel)

Sample of the ‘Abri de Pendimoun’ different stratigraphical units (US)
SiteName Country Period PhaseCode LabCode C14Age C14SD Material
Abri Pendimoun France EN US 41678 LTL-8005A 6599 45 cereal
Abri Pendimoun France EN US 42370 LTL-8009A 6241 45 plant seed
Abri Pendimoun France EN US 18364 LTL-8012A 6499 45 plant seed
Abri Pendimoun France MN US 14647 GrA-32944 6275 40 plant seed
Abri Pendimoun France EN US 18364 LTL-8011A 6507 45 plant seed

3.1.2 How to contribute to the dataset

The next NeoNet dataset aims to cover the Middle and Southern European Atlantic watershed (ie. western Iberian peninsula and Western France)

Preview of the next NeoNet C14 dates dataset, in blue, covering the Middle and Southern European Atlantic watershed

Preview of the next NeoNet C14 dates dataset, in blue, covering the Middle and Southern European Atlantic watershed

4 Acknowledgement

We are especially thankful to Federico Bianchi of the University of Pisa for the technical support